Contacts of the helix formed by residues 295 - 303 (chain A) in PDB entry 2OT7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU* 2.9 35.1 + - - -
40A HIS* 3.4 29.7 - - - +
195A TYR* 3.6 6.5 + - - +
213A PRO* 6.3 0.6 - - - +
271A PHE* 3.9 2.0 - - - +
272A PRO* 3.8 18.8 + - - +
293A THR* 3.2 5.4 - - - +
294A ARG* 1.3 76.9 - - - +
296A TRP* 1.3 61.5 + - - +
297A ILE 3.2 0.7 + - - -
298A GLU* 3.7 9.7 + - - +
299A TYR* 3.1 53.0 + - + -
342A ASP 5.4 1.3 + - - -
343A HIS* 4.6 3.4 + - - +
345A LEU* 3.1 24.9 + - - -
346A PRO 3.6 2.7 - - - +
347A THR* 3.2 30.9 + - - +
348A PRO* 4.0 6.1 - - + +
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Residues in contact with TRP 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ILE* 5.1 0.2 - - + -
157A LEU* 5.0 0.7 - - + -
192A MET* 2.9 32.9 + - + -
193A ASP 3.3 22.1 + - - -
194A LEU* 3.2 34.9 - - + +
195A TYR* 4.0 18.8 - - + -
272A PRO* 4.4 3.1 - - + -
292A ALA* 3.7 15.5 - - + -
293A THR* 3.2 14.0 + - - +
294A ARG 3.1 1.2 - - - -
295A ARG* 1.3 76.6 - - - +
297A ILE* 1.3 75.9 + - + +
299A TYR* 2.9 13.8 + - + -
300A GLY* 2.8 26.4 + - - +
315A ILE* 4.6 8.1 - - + -
317A MET* 3.4 40.2 - - + -
320A PHE* 3.8 35.2 - + - -
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Residues in contact with ILE 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ILE* 4.0 14.1 - - + -
294A ARG* 3.7 16.8 - - + +
295A ARG 3.2 2.0 - - - -
296A TRP* 1.3 93.2 - - + +
298A GLU* 1.3 56.6 + - - +
300A GLY 3.3 0.5 + - - -
301A LYS* 3.0 32.3 + - + +
317A MET* 3.4 13.7 - - + +
320A PHE* 3.9 28.3 - - + +
321A VAL* 4.5 1.3 - - + -
324A PHE* 3.6 43.1 - - + -
325A GLN* 3.7 27.6 - - + +
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ARG 4.7 0.4 + - - -
295A ARG 3.7 8.3 + - - +
296A TRP 3.2 0.8 - - - -
297A ILE* 1.3 75.8 - - - +
299A TYR* 1.3 66.3 + - + +
301A LYS* 3.0 37.9 + - - +
302A GLN* 2.9 60.2 + - - +
325A GLN* 3.3 15.9 + - - +
328A ARG* 5.3 1.7 - - - -
337A ASP* 4.6 2.8 - - - +
339A THR* 3.6 28.4 + - + +
341A ILE* 3.8 16.2 - - + -
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Residues in contact with TYR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A MET 4.2 2.4 - - - +
193A ASP* 4.2 10.8 - - + +
213A PRO* 4.9 1.2 - - - +
272A PRO* 3.5 33.8 + - + -
273A TYR* 3.8 13.0 - + + -
295A ARG* 3.1 55.0 + - + -
296A TRP* 2.9 18.1 + - + +
298A GLU* 1.3 78.4 - - + +
300A GLY* 1.3 57.1 + - - +
302A GLN* 3.3 1.6 + - - +
303A ALA* 2.9 31.0 + - - +
341A ILE* 3.5 28.5 - - + +
342A ASP 4.6 0.8 + - - -
343A HIS* 2.7 47.8 + + - +
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Residues in contact with GLY 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A MET* 3.5 34.2 - - - +
296A TRP* 2.8 22.7 + - - +
297A ILE 3.3 4.0 + - - -
299A TYR* 1.3 75.5 - - - +
301A LYS* 1.3 61.5 + - - +
302A GLN 3.4 0.2 + - - -
303A ALA* 3.7 7.3 + - - +
317A MET* 3.8 18.4 - - - +
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Residues in contact with LYS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A ILE* 3.0 22.3 + - + +
298A GLU* 3.0 35.1 + - - +
300A GLY* 1.3 75.9 - - - +
302A GLN* 1.3 61.0 + - + +
303A ALA 3.6 1.1 + - - +
317A MET* 3.9 11.6 - - + +
321A VAL* 3.7 18.7 - - + +
325A GLN* 2.7 29.2 + - - +
328A ARG* 4.7 1.0 - - - +
332A TRP* 3.4 42.6 + - + +
337A ASP* 2.7 26.6 + - - -
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Residues in contact with GLN 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A GLU* 2.9 44.4 + - - +
299A TYR 3.6 2.5 - - - +
301A LYS* 1.3 80.4 - - + +
303A ALA* 1.3 66.2 + - - +
304A VAL* 3.2 12.1 + - - +
337A ASP 5.6 1.4 + - - -
339A THR* 2.7 30.0 + - - +
340A VAL* 5.3 0.2 - - - -
341A ILE* 3.7 24.0 + - + +
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A MET* 4.0 18.8 - - + -
193A ASP* 3.7 18.8 - - - +
239A ARG* 4.1 2.0 - - - +
299A TYR 2.9 16.6 + - - +
300A GLY 3.7 10.8 + - - +
301A LYS 3.6 3.1 - - - +
302A GLN* 1.3 76.2 - - - +
304A VAL* 1.3 60.8 + - - +
305A LEU* 3.5 27.7 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il